data_2GZH # _model_server_result.job_id pY8WSYuWYr1jlcxnLWwNMQ _model_server_result.datetime_utc '2024-11-26 03:59:29' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 2gzh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":900}' # _entry.id 2GZH # _exptl.entry_id 2GZH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.18 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 2GZH _cell.length_a 64.74 _cell.length_b 64.74 _cell.length_c 112.4 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GZH _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_555 x-y,-y,-z+2/3 1 0 0 0 -1 0 0 0 -1 0 0 74.933333 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 A C ILE 119 A ILE 119 1_555 A N MSE 120 A MSE 120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale2 A C MSE 120 A MSE 120 1_555 A N LEU 121 A LEU 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 B C VAL 83 B VAL 488 1_555 B N MSE 84 B MSE 489 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale4 B C MSE 84 B MSE 489 1_555 B N GLU 85 B GLU 490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? metalc ? metalc1 A OG SER 25 A SER 25 1_555 D MG MG . A MG 950 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc2 A OG1 THR 43 A THR 43 1_555 D MG MG . A MG 950 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc3 G O HOH . A HOH 648 1_555 E MG MG . A MG 951 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.901 ? metalc ? metalc4 G O HOH . A HOH 655 1_555 D MG MG . A MG 950 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? metalc ? metalc5 G O HOH . A HOH 657 1_555 E MG MG . A MG 951 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc6 G O HOH . A HOH 658 1_555 D MG MG . A MG 950 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc7 F O2B GTP . A GTP 900 1_555 D MG MG . A MG 950 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc8 F O2G GTP . A GTP 900 1_555 D MG MG . A MG 950 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? # _chem_comp.formula 'C10 H16 N5 O14 P3' _chem_comp.formula_weight 523.18 _chem_comp.id GTP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-TRIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag PG O1G GTP doub 116 n n PG O2G GTP sing 117 n n PG O3G GTP sing 118 n n PG O3B GTP sing 119 n n O2G HOG2 GTP sing 120 n n O3G HOG3 GTP sing 121 n n O3B PB GTP sing 122 n n PB O1B GTP doub 123 n n PB O2B GTP sing 124 n n PB O3A GTP sing 125 n n O2B HOB2 GTP sing 126 n n O3A PA GTP sing 127 n n PA O1A GTP doub 128 n n PA O2A GTP sing 129 n n PA O5' GTP sing 130 n n O2A HOA2 GTP sing 131 n n O5' C5' GTP sing 132 n n C5' C4' GTP sing 133 n n C5' H5' GTP sing 134 n n C5' "H5''" GTP sing 135 n n C4' O4' GTP sing 136 n n C4' C3' GTP sing 137 n n C4' H4' GTP sing 138 n n O4' C1' GTP sing 139 n n C3' O3' GTP sing 140 n n C3' C2' GTP sing 141 n n C3' H3' GTP sing 142 n n O3' HO3' GTP sing 143 n n C2' O2' GTP sing 144 n n C2' C1' GTP sing 145 n n C2' H2' GTP sing 146 n n O2' HO2' GTP sing 147 n n C1' N9 GTP sing 148 n n C1' H1' GTP sing 149 n n N9 C8 GTP sing 150 n y N9 C4 GTP sing 151 n y C8 N7 GTP doub 152 n y C8 H8 GTP sing 153 n n N7 C5 GTP sing 154 n y C5 C6 GTP sing 155 n n C5 C4 GTP doub 156 n y C6 O6 GTP doub 157 n n C6 N1 GTP sing 158 n n N1 C2 GTP sing 159 n n N1 HN1 GTP sing 160 n n C2 N2 GTP sing 161 n n C2 N3 GTP doub 162 n n N2 HN21 GTP sing 163 n n N2 HN22 GTP sing 164 n n N3 C4 GTP sing 165 n n # _atom_sites.entry_id 2GZH _atom_sites.fract_transf_matrix[1][1] 0.015446 _atom_sites.fract_transf_matrix[1][2] 0.008918 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017836 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.008897 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 3 PO4 A 1 901 901 PO4 PO4 . D 4 MG A 1 950 950 MG MG . E 4 MG A 1 951 951 MG MG . F 5 GTP A 1 900 900 GTP GTP . G 6 HOH A 1 503 503 HOH HOH . G 6 HOH A 2 505 505 HOH HOH . G 6 HOH A 3 508 508 HOH HOH . G 6 HOH A 4 509 509 HOH HOH . G 6 HOH A 5 510 510 HOH HOH . G 6 HOH A 6 511 511 HOH HOH . G 6 HOH A 7 512 512 HOH HOH . G 6 HOH A 8 513 513 HOH HOH . G 6 HOH A 9 514 514 HOH HOH . G 6 HOH A 10 515 515 HOH HOH . G 6 HOH A 11 516 516 HOH HOH . G 6 HOH A 12 517 517 HOH HOH . G 6 HOH A 13 518 518 HOH HOH . G 6 HOH A 14 519 519 HOH HOH . G 6 HOH A 15 521 521 HOH HOH . G 6 HOH A 16 524 524 HOH HOH . G 6 HOH A 17 525 525 HOH HOH . G 6 HOH A 18 526 526 HOH HOH . G 6 HOH A 19 527 527 HOH HOH . G 6 HOH A 20 528 528 HOH HOH . G 6 HOH A 21 529 529 HOH HOH . G 6 HOH A 22 530 530 HOH HOH . G 6 HOH A 23 531 531 HOH HOH . G 6 HOH A 24 532 532 HOH HOH . G 6 HOH A 25 533 533 HOH HOH . G 6 HOH A 26 534 534 HOH HOH . G 6 HOH A 27 535 535 HOH HOH . G 6 HOH A 28 536 536 HOH HOH . G 6 HOH A 29 538 538 HOH HOH . G 6 HOH A 30 539 539 HOH HOH . G 6 HOH A 31 540 540 HOH HOH . G 6 HOH A 32 541 541 HOH HOH . G 6 HOH A 33 542 542 HOH HOH . G 6 HOH A 34 543 543 HOH HOH . G 6 HOH A 35 544 544 HOH HOH . G 6 HOH A 36 546 546 HOH HOH . G 6 HOH A 37 547 547 HOH HOH . G 6 HOH A 38 548 548 HOH HOH . G 6 HOH A 39 549 549 HOH HOH . G 6 HOH A 40 550 550 HOH HOH . G 6 HOH A 41 551 551 HOH HOH . G 6 HOH A 42 552 552 HOH HOH . G 6 HOH A 43 553 553 HOH HOH . G 6 HOH A 44 554 554 HOH HOH . G 6 HOH A 45 555 555 HOH HOH . G 6 HOH A 46 557 557 HOH HOH . G 6 HOH A 47 558 558 HOH HOH . G 6 HOH A 48 559 559 HOH HOH . G 6 HOH A 49 560 560 HOH HOH . G 6 HOH A 50 562 562 HOH HOH . G 6 HOH A 51 563 563 HOH HOH . G 6 HOH A 52 564 564 HOH HOH . G 6 HOH A 53 565 565 HOH HOH . G 6 HOH A 54 568 568 HOH HOH . G 6 HOH A 55 570 570 HOH HOH . G 6 HOH A 56 571 571 HOH HOH . G 6 HOH A 57 572 572 HOH HOH . G 6 HOH A 58 573 573 HOH HOH . G 6 HOH A 59 574 574 HOH HOH . G 6 HOH A 60 575 575 HOH HOH . G 6 HOH A 61 576 576 HOH HOH . G 6 HOH A 62 577 577 HOH HOH . G 6 HOH A 63 578 578 HOH HOH . G 6 HOH A 64 579 579 HOH HOH . G 6 HOH A 65 580 580 HOH HOH . G 6 HOH A 66 581 581 HOH HOH . G 6 HOH A 67 582 582 HOH HOH . G 6 HOH A 68 583 583 HOH HOH . G 6 HOH A 69 584 584 HOH HOH . G 6 HOH A 70 585 585 HOH HOH . G 6 HOH A 71 586 586 HOH HOH . G 6 HOH A 72 587 587 HOH HOH . G 6 HOH A 73 588 588 HOH HOH . G 6 HOH A 74 589 589 HOH HOH . G 6 HOH A 75 590 590 HOH HOH . G 6 HOH A 76 591 591 HOH HOH . G 6 HOH A 77 592 592 HOH HOH . G 6 HOH A 78 593 593 HOH HOH . G 6 HOH A 79 594 594 HOH HOH . G 6 HOH A 80 595 595 HOH HOH . G 6 HOH A 81 596 596 HOH HOH . G 6 HOH A 82 597 597 HOH HOH . G 6 HOH A 83 598 598 HOH HOH . G 6 HOH A 84 600 600 HOH HOH . G 6 HOH A 85 601 601 HOH HOH . G 6 HOH A 86 602 602 HOH HOH . G 6 HOH A 87 603 603 HOH HOH . G 6 HOH A 88 604 604 HOH HOH . G 6 HOH A 89 605 605 HOH HOH . G 6 HOH A 90 606 606 HOH HOH . G 6 HOH A 91 607 607 HOH HOH . G 6 HOH A 92 608 608 HOH HOH . G 6 HOH A 93 609 609 HOH HOH . G 6 HOH A 94 610 610 HOH HOH . G 6 HOH A 95 611 611 HOH HOH . G 6 HOH A 96 613 613 HOH HOH . G 6 HOH A 97 615 615 HOH HOH . G 6 HOH A 98 616 616 HOH HOH . G 6 HOH A 99 617 617 HOH HOH . G 6 HOH A 100 620 620 HOH HOH . G 6 HOH A 101 622 622 HOH HOH . G 6 HOH A 102 623 623 HOH HOH . G 6 HOH A 103 626 626 HOH HOH . G 6 HOH A 104 628 628 HOH HOH . G 6 HOH A 105 629 629 HOH HOH . G 6 HOH A 106 631 631 HOH HOH . G 6 HOH A 107 632 632 HOH HOH . G 6 HOH A 108 633 633 HOH HOH . G 6 HOH A 109 641 641 HOH HOH . G 6 HOH A 110 644 644 HOH HOH . G 6 HOH A 111 645 645 HOH HOH . G 6 HOH A 112 647 647 HOH HOH . G 6 HOH A 113 648 648 HOH HOH . G 6 HOH A 114 649 649 HOH HOH . G 6 HOH A 115 650 650 HOH HOH . G 6 HOH A 116 651 651 HOH HOH . G 6 HOH A 117 652 652 HOH HOH . G 6 HOH A 118 653 653 HOH HOH . G 6 HOH A 119 654 654 HOH HOH . G 6 HOH A 120 655 655 HOH HOH . G 6 HOH A 121 656 656 HOH HOH . G 6 HOH A 122 657 657 HOH HOH . G 6 HOH A 123 658 658 HOH HOH . G 6 HOH A 124 659 659 HOH HOH . H 6 HOH B 1 627 627 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P PG GTP . . . F 5 31.004 8.773 25.008 1 43.9 ? PG GTP 900 A 1 HETATM 2 O O1G GTP . . . F 5 32.094 8.002 25.688 1 42.8 ? O1G GTP 900 A 1 HETATM 3 O O2G GTP . . . F 5 29.919 8.855 26.069 1 38.67 ? O2G GTP 900 A 1 HETATM 4 O O3G GTP . . . F 5 30.553 7.889 23.846 1 40.08 ? O3G GTP 900 A 1 HETATM 5 O O3B GTP . . . F 5 31.532 10.351 24.499 1 40.12 ? O3B GTP 900 A 1 HETATM 6 P PB GTP . . . F 5 30.597 11.519 23.772 1 30.16 ? PB GTP 900 A 1 HETATM 7 O O1B GTP . . . F 5 30.38 11.195 22.311 1 33.07 ? O1B GTP 900 A 1 HETATM 8 O O2B GTP . . . F 5 29.197 11.589 24.324 1 34.75 ? O2B GTP 900 A 1 HETATM 9 O O3A GTP . . . F 5 31.117 13.016 23.618 1 33.63 ? O3A GTP 900 A 1 HETATM 10 P PA GTP . . . F 5 30.916 14.214 24.652 1 33.25 ? PA GTP 900 A 1 HETATM 11 O O1A GTP . . . F 5 29.594 14.966 24.513 1 35.83 ? O1A GTP 900 A 1 HETATM 12 O O2A GTP . . . F 5 31.132 13.684 26.038 1 34.39 ? O2A GTP 900 A 1 HETATM 13 O O5' GTP . . . F 5 32.123 15.173 24.28 1 33.11 ? O5' GTP 900 A 1 HETATM 14 C C5' GTP . . . F 5 33.44 14.655 24.272 1 33.04 ? C5' GTP 900 A 1 HETATM 15 C C4' GTP . . . F 5 34.415 15.826 24.381 1 37.31 ? C4' GTP 900 A 1 HETATM 16 O O4' GTP . . . F 5 34.389 16.699 23.248 1 35.07 ? O4' GTP 900 A 1 HETATM 17 C C3' GTP . . . F 5 34.096 16.692 25.58 1 38.19 ? C3' GTP 900 A 1 HETATM 18 O O3' GTP . . . F 5 35.342 17.146 26.033 1 44.2 ? O3' GTP 900 A 1 HETATM 19 C C2' GTP . . . F 5 33.334 17.846 24.979 1 37.12 ? C2' GTP 900 A 1 HETATM 20 O O2' GTP . . . F 5 33.496 19.058 25.653 1 38.96 ? O2' GTP 900 A 1 HETATM 21 C C1' GTP . . . F 5 33.956 17.985 23.626 1 35.13 ? C1' GTP 900 A 1 HETATM 22 N N9 GTP . . . F 5 32.932 18.419 22.662 1 36.78 ? N9 GTP 900 A 1 HETATM 23 C C8 GTP . . . F 5 31.647 17.94 22.454 1 35.72 ? C8 GTP 900 A 1 HETATM 24 N N7 GTP . . . F 5 31.119 18.636 21.42 1 34.64 ? N7 GTP 900 A 1 HETATM 25 C C5 GTP . . . F 5 32.032 19.529 20.965 1 36.19 ? C5 GTP 900 A 1 HETATM 26 C C6 GTP . . . F 5 32.029 20.517 19.948 1 36.31 ? C6 GTP 900 A 1 HETATM 27 O O6 GTP . . . F 5 31.034 20.725 19.205 1 35.39 ? O6 GTP 900 A 1 HETATM 28 N N1 GTP . . . F 5 33.192 21.274 19.781 1 35.53 ? N1 GTP 900 A 1 HETATM 29 C C2 GTP . . . F 5 34.299 21.109 20.594 1 35.86 ? C2 GTP 900 A 1 HETATM 30 N N2 GTP . . . F 5 35.397 21.834 20.405 1 36.79 ? N2 GTP 900 A 1 HETATM 31 N N3 GTP . . . F 5 34.29 20.147 21.583 1 35.5 ? N3 GTP 900 A 1 HETATM 32 C C4 GTP . . . F 5 33.176 19.389 21.753 1 35.29 ? C4 GTP 900 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 32 #